The area declared an emergency on Saturday night after heavy rainfall was reported. The storm that lashed Bavaria and Saxony exacerbated the extreme weather crisis that has left dozens dead across Germany.
"We have two dead… We know that one person died of a natural cause, which in some way may be related to the storm," Bernhard Kern told a news conference in Bad Reichenhall.
Kern said emergency services had been dealing with the aftermath of the storm since late Saturday. He urged travelers to avoid the district.
At least 156 people have died in Germany since Tuesday after catastrophic floods blamed on global warming swept the country’s western states of North Rhine-Westphalia and Rhineland-Palatinate.